1MHZ

METHANE MONOOXYGENASE HYDROXYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b

Elango, N.Radhakrishnan, R.Froland, W.A.Wallar, B.J.Earhart, C.A.Lipscomb, J.D.Ohlendorf, D.H.

(1997) Protein Sci. 6: 556-568

  • DOI: 10.1002/pro.5560060305
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the O2-dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory "B" component (MMOB), a ...

    Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the O2-dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory "B" component (MMOB), and a hydroxylase component (MMOH), which contains a hydroxo-bridged dinuclear iron cluster. Two genera of methanotrophs, termed Type X and Type II, which differ markedly in cellular and metabolic characteristics, are known to produce the sMMO. The structure of MMOH from the Type X methanotroph Methylococcus capsulatus Bath (MMO Bath) has been reported recently. Two different structures were found for the essential diiron cluster, depending upon the temperature at which the diffraction data were collected. In order to extend the structural studies to the Type II methanotrophs and to determine whether one of the two known MMOH structures is generally applicable to the MMOH family, we have determined the crystal structure of the MMOH from Type II Methylosinus trichosporium OB3b (MMO OB3b) in two crystal forms to 2.0 A resolution, respectively, both determined at 18 degrees C. The crystal forms differ in that MMOB was present during crystallization of the second form. Both crystal forms, however, yielded very similar results for the structure of the MMOH. Most of the major structural features of the MMOH Bath were also maintained with high fidelity. The two irons of the active site cluster of MMOH OB3b are bridged by two OH (or one OH and one H2O), as well as both carboxylate oxygens of Glu alpha 144. This bis-mu-hydroxo-bridged "diamond core" structure, with a short Fe-Fe distance of 2.99 A, is unique for the resting state of proteins containing analogous diiron clusters, and is very similar to the structure reported for the cluster from flash frozen (-160 degrees C) crystals of MMOH Bath, suggesting a common active site structure for the soluble MMOHs. The high-resolution structure of MMOH OB3b indicates 26 consecutive amino acid sequence differences in the beta chain when compared to the previously reported sequence inferred from the cloned gene. Fifteen additional sequence differences distributed randomly over the three chains were also observed, including D alpha 209E, a ligand of one of the irons.


    Organizational Affiliation

    Department of Biochemistry, Medical School, University of Minnesota, Minneapolis 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHANE MONOOXYGENASE HYDROXYLASE
B
395Methylosinus trichosporiumMutation(s): 0 
Gene Names: mmoY
EC: 1.14.13.25
Find proteins for P27354 (Methylosinus trichosporium)
Go to UniProtKB:  P27354
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHANE MONOOXYGENASE HYDROXYLASE
D
521Methylosinus trichosporiumMutation(s): 0 
Gene Names: mmoX
EC: 1.14.13.25
Find proteins for P27353 (Methylosinus trichosporium)
Go to UniProtKB:  P27353
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
METHANE MONOOXYGENASE HYDROXYLASE
G
169Methylosinus trichosporiumMutation(s): 0 
Gene Names: mmoZ
EC: 1.14.13.25
Find proteins for P27355 (Methylosinus trichosporium)
Go to UniProtKB:  P27355
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.152 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 293.380α = 90.00
b = 64.010β = 90.00
c = 143.650γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
XENGENdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other